So even to this day science cannot explain dreams, or how the human brain fully works.
What are you on?
Does that mean it doesn't exist?
... my mistake, what were you supposed to be on?
Or how people were flatlined during surgery for 10 seconds before the heart started beating again?
I assume you mean OBE: vivid hallucinations.
Or what about our self awareness? How are you able to recognize that you are here and breathing?
I have a combination of neural systems that, when combined within the structural realities of time and space, permit me to have some sort of memory and retrospective sense which gives this feeling. The feeling that you can see your past actions and their consequences, and maybe influence your future unconscious actions in a retrospectively informed manner, is what underpins the illusion of free will.
Who gave you that self consciousness?
The error in your process creeps in here.
Or if nobody gave you, how did that come to fruition?
Evolution. Genetic algorithms. Algorithms we may not have discovered yet. Look what folding models have done to protein folding research lately.
Why are we not like other animals that only follow their instinct and don't actually ponder in philosophical questions?
Certain primates show more control than other mammals. Arguably Co-co had a higher intelligence quotient than the average African. Most mammals, I think, are stuck at around a human toddler's level of cognitive function, with some specialized advancements (kinesthetic, etc). They may not ponder like us because they lack a complex enough language and abstraction ability. We only really deal with a handful of objects in our active minds at any moment, it's the power of abstraction which permits us to put ideas into ideas like Matry0shka dolls.